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Sample GSM3315902 Query DataSets for GSM3315902
Status Public on Sep 19, 2018
Title Sca1- Adventitial pooled rep 3
Sample type SRA
 
Source name Adventitial layer of mouse aorta
Organism Mus musculus
Characteristics region: Aorta
genotype: wild type
cell type: Adventitial cells
background: C57Bl/6
Extracted molecule total RNA
Extraction protocol Pooled samples were prepared from the cell suspension used for Fluidigm C1 analysis of single cells. Total RNA was extracted from 2000-4000 cells using the Qiagen RNeasy Plus Micro Kit.
RNA from 100-200 cells was used to generate amplified cDNA using the SMARTer® Ultra™ Low RNA Kit (Clontech) following the protocol for tube controls. Sequencing libraries were made from 0.125-0.375 ng amplified cDNA using the Nextera XT library preparation kit (Illumina).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description pooled RNA-seq
normalised_pooled_counts.txt
Data processing Samples 1 - 313: Raw reads were trimmed using TrimGalore and Cutadapt. Alignment of the reads to the GRCm38 genome was performed using TopHat. Reads per gene were counted using htseq-count (single-cell RNA-seq) or Seqmonk (bulk RNA-seq). Reads were normalised using DESeq2 (bulk RNA-seq) or the scran Bioconductor R package (sinlge-cell RNA-seq) using the computeSumFactors function.
Samples 314 - 317: Raw sequencing data were processed through the 10X genomics Cellranger pipeline (v2). Cellranger demultiplexed the raw sequencing data, produced the fastq files, aligned the reads to the mouse genome (mm10, STAR aligner) performed unique molecular identifier (UMI) counting.
Genome_build: mm10
Supplementary_files_format_and_content: Samples 1 - 313: Tab separated text files contain normalised read counts with genes in rows and cells/samples in columns. Samples 314 - 317: Filtered gene barcode matrices output by the 10X genomics Cellranger pipeline in the h5 format (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/h5_matrices)
 
Submission date Jul 31, 2018
Last update date Sep 19, 2018
Contact name Steven William Wingett
E-mail(s) steven.wingett@mrc-lmb.cam.ac.uk
Organization name MRC Laboratory of Molecular Biology
Department Cell Biology
Street address Francis Crick Avenue, Cambridge Biomedical Campus
City Cambridge
State/province Cambs
ZIP/Postal code CB2 0QH
Country United Kingdom
 
Platform ID GPL17021
Series (1)
GSE117963 Disease-relevant transcriptional signatures identified in individual smooth muscle cells from healthy mouse vessels
Relations
BioSample SAMN09745552
SRA SRX4493184

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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